Kaipara resumed the day on 147 and kicked on to 167 for nine before declaring with a slim lead over City.
However, City couldn't break the stalemate and were bowled out cheaply for 55, leaving Kaipara only 53 to win.
Matt Taylor was the pick of the bowlers with his four for 10, complemented well by Kevin Forde, who claimed four for 11.
Chasing 53, Kaipara's opening batsmen did the damage as they reached the target with only one wicket down.
In Whangarei Boys' High School's match, they were left demoralised by Onerahi on the second day, as they went down by an innings and 71 runs.